In vitro regeneration systems either based on organogenesis or somatic embryogenesis has been well established in Carica papaya L. Whereas a third morphogenetic pathway involving plant regeneration system through nodular cultures have not been reported. Here, we report an efficient and rapid in vitro regeneration system through callus derived nodular culture in papaya cultivar CO7. Excised zygotic embryos were cultured onto Murashige and Skoog (MS) medium supplemented with different concentrations and combinations of auxins and cytokinins. Maximum response from explants producing callus (82.30%) was observed on MS medium with 2.0 mg/l of 2, 4, 5 trichlorophenoxyacetic acid (2, 4, 5-T), whereas a high frequency of nodulation (62.30%) was induced on MS medium containing 1.0 mg/l of 2, 4, 5-T. Nodules were separated from callus cultures and transferred onto MS medium fortified with 0.4 mg/l BAP (6-benzylaminopurine) and 0.04 mg/l NAA (α-naphthaleneacetic acid) showed regeneration efficiency of up to 62.22%. The healthy elongated shoots with 2–3 trilobed leaves were successfully rooted (72.12%) on a half-strength MS medium containing 1.0 mg/l indole-3-butyric acid (IBA) with an average root numbers 4.0 ± 1.2. The histochemical analysis of nodules authenticates the distinctive anatomy exhibiting the vascular elements bounded with the cortex and epidermal layering. In the present study, morphogenetic features of papaya regeneration through nodular cultures reveal distinct characteristics from organogenesis and somatic embryogenesis.